（See my ResearchGate profile for most recent updates）

Zhou, Jiayin, Wei Qin, Xinda Lu, Yunfeng Yang, David A. Stahl, Nianzhi Jiao, Jizhong Zhou, Jihua Liu and Qichao Tu*. “The diversity and ecological significance of microbial traits potentially involved in B12 biosynthesis in the global ocean.” mLife. 2023. 2(4):416-427. https://doi.org/10.1002/mlf2.12095

Song W, Li H, Zhou Y, Liu X, Li Y, Wang M, Li D-d and Tu Q* (2023) Discordant patterns between nitrogen-cycling functional traits and taxa in distant coastal sediments reveal important community assembly mechanisms. Front. Microbiol. 14:1291242. doi: 10.3389/fmicb.2023.1291242

Ma K, Li Y, Liu X, Song W, Zhou J, Gong X, Wang M, Li C, Liu J, Tu Q*. Bacteria rather than fungi mediate the chemodiversity of dissolved organic matter in a mudflat intertidal zone. Sci Total Environ. 2023 Oct 1;893:164835. doi: 10.1016/j.scitotenv.2023.164835.

Li Y, Ma K, Song W, Zhou J, Liu X, Wang M, Tu Q*. Environmental heterogeneity and dispersal limitation simultaneously determine the spatial scaling of different microbial functional groups. Sci Total Environ. 2023 May 3;885:163854. doi: 10.1016/j.scitotenv.2023.163854.

Liu, X., Li, H., Song, W., & Tu, Q*. (2023). Distinct ecological mechanisms drive the spatial scaling of abundant and rare taxa in a coastal sediment. Journal of Biogeography. https://doi.org/10.1111/ jbi.14584

Xiaofan Gong, Xia Liu, Yueyue Li, Kai Ma, Wen Song, Jiayin Zhou, Qichao Tu*. (2023). Distinct ecological processes mediate domain-level differentiation in microbial spatial scaling. Applied and Environmental Microbiology. https://doi.org/10.1128/aem.02096-22

Zhou J, Song W, and Tu Q*. (2023). To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities. Briefings in Bioinformatics. 24(1): bbac594. https://doi.org/10.1093/bib/bbac594

Ma K and Tu Q*. (2022). Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly. Front. Microbiol. 13:1011269. doi: 10.3389/fmicb.2022.1011269

Wang M and Tu Q*. (2022). Effective data filtering is prerequisite for robust microbial association network construction. Front. Microbiol. 13:1016947. doi: 10.3389/fmicb.2022.1016947

Chun Li, Jihua Liu*, Xiao Chen, Hongwei Ren, Bei Su, Kai Ma, Qichao Tu*.  (2022). Determinism governs the succession of disturbed bacterioplankton communities in a coastal maricultural ecosystem. Science of the Total Environment. 128(1):154457.  https://doi.org/10.1016/j.scitotenv.2022.154457

Wen Song, Jihua Liu*, Wei Qin, Jun Huang, Xiaoli Yu, Mengzhao Xu, David Stahl, Nianzhi Jiao, Jizhong Zhou, Qichao Tu*. (2022). Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean. mBio. 13(2):e0383221. https://doi.org/10.1128/mbio.03832-21

Lu Qian, Xiaoli Yu, Jiayin Zhou, Hang Gu, Jijuan Ding, Yisheng Peng, Qiang He, Yun Tian, Jihua Liu, Shanquan Wang, Cheng Wang, Longfei Shu, Qingyun Yan, Jianguo He, Guangli Liu*, Qichao Tu*, Zhili He*. (2022). MCycDB: A curated database for comprehensively profiling methane cycling processes of environmental microbiomes. Molecular Ecology Resources. 22(5):1803-1823 https://doi.org/10.1111/1755-0998.13589

Zhou J, Yu X, Liu J, Qin W, He Z, Stahl D, Jiao N, Zhou J, Tu Q^*. (2021). VB₁₂Path for Accurate Metagenomic Profiling of Microbially Driven Cobalamin Synthesis Pathways. mSystems. 6(3):e0049721.

Xu, M., Xu, M.*, and Tu, Q.* 2021. Comparative evaluation of Vibrio delineation methodologies in post-genomic era. Environmental Microbiology Reports. 13(2):209-217.  https://doi.org/10.1111/1758-2229.12928

Yu, X., Zhou, J., Song, W., Xu, M., He, Q., Peng, Y., Tian, Y., Wang, C., Shu, L., Wang, S., Yan, Q., Liu, J., Tu, Q.^* and He, Z^*. (2021), SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways. Mol Ecol Resour. 21(3):924-940. https://doi.org/10.1111/1755-0998.13306

Qichao Tu^*, Qingyun Yan, Ye Deng, Sean T. Michaletz, Vanessa Buzzard, Michael D. Weiser, Robert Waide, Daliang Ning, Liyou Wu, Zhili He, and Jizhong Zhou^*. 2020. “Biogeographic Patterns of Microbial Co-Occurrence Ecological Networks in Six American Forests.” Soil Biology & Biochemistry 148: 107897.

Qichao Tu^*. 2020. “Random Sampling in Metagenomic Sequencing Leads to Overestimated Spatial Scaling of Microbial Diversity.” Environmental Microbiology 22 (6): 2140–49.

Qichao Tu^*, Lu Lin^*, Lei Cheng, Ye Deng, and Zhili He. 2019. “NCycDB: A Curated Integrative Database for Fast and Accurate Metagenomic Profiling of Nitrogen Cycling Genes.” Bioinformatics 35 (6): 1040–48.

Qichao Tu, Zhili He, Liyou Wu, Kai Xue, Gary Xie, Patrick Chain, Peter B. Reich, Sarah E. Hobbie, and Jizhong Zhou^*. 2017. “Metagenomic Reconstruction of Nitrogen Cycling Pathways in a CO2-Enriched Grassland Ecosystem.” Soil Biology & Biochemistry 106: 99–108.

Jinzhi He#, Qichao Tu#, Yichen Ge, Yujia Qin, Bomiao Cui, Xiaoyu Hu, Yuxia Wang, Ye Deng, Kun Wang, Joy D. Van Nostrand, Jiyao Li, Jizhong Zhou, Yan Li, Xuedong Zhou. Taxonomic and Functional Analyses of the Supragingival Microbiome from Caries-Affected and Caries-Free Hosts. Microbial Ecology, 2017. (# equal contribution)

Tu, Qichao; Li, Jiabao; Shi, Zhou; Chen, Yanfei; Lin, Lu; Li, Juan; Wang, Hongling; Yan, Jianbo; Zhou, Qingming; Li, Xiangzhen; Li, Lanjuan; Zhou, Jizhong*; He, Zhili*. HuMiChip2 for strain level identification and functional profiling of human microbiomes. Appl Microbiol Biotechnol, 101(1), pp 423-435, 2017/1.

Qichao Tu, and Lu Lin*. 2016. “Gene Content Dissimilarity for Subclassification of Highly Similar Microbial Strains.” BMC Genomics 17 (1): 647–647.

Qichao Tu, Ye Deng, Qingyun Yan, Lina Shen, Lu Lin, Zhili He, Liyou Wu, Joy D. Van Nostrand, Vanessa Buzzard, Sean T. Michaletz, Brian J. Enquist, Michael D. Weiser, Michael Kaspari, Robert B. Waide, James H. Brown , and Jizhong Zhou*. 2016. “Biogeographic Patterns of Soil Diazotrophic Communities across Six Forests in the North America.” Molecular Ecology 25 (12): 2937–48.

Qichao Tu, Xishu Zhou, Zhili He, Liyou Wu, Peter Reich, Sarah Hobbie, and Jizhong Zhou*. The diversity and co-occurrence patterns of N2-fixing microbial communities in a CO2-enriched grassland soil ecosystem. Microbial Ecology.  (2016) 71(3):604-15

Qichao Tu, Mengting Yuan, Zhili He, Ye Deng, Liyou Wu, Sara E. Hobbie, Peter B. Reich, and Jizhong Zhou*. “Fungal communities respond to long-term CO2 elevation by community reassembly.” Applied and Environmental Microbiology. (2015) 81(7): 2445-2454.

Qichao Tu, Hao Yu, Zhili He, Ye Deng, Liyou Wu, Joy D. Van Nostrand, Aifen Zhou, James Voordeckers, Yong-Jin Lee, Yujia Qin, Christopher L. Hemme, Zhou Shi, Kai Xue, Tong Yuan, Aijie Wang, Jizhong Zhou*. 2014. “GeoChip 4: A Functional Gene-Array-Based High-Throughput Environmental Technology for Microbial Community Analysis.” Molecular Ecology Resources 14 (5): 914–28.

Qichao Tu, Zhili He*, and Jizhong Zhou*. 2014. “Strain/Species Identification in Metagenomes Using Genome-Specific Markers.” Nucleic Acids Research 42 (8).

Qichao Tu, Zhili He, Yan Li, Yanfei Chen, Ye Deng, Lu Lin, Christopher L. Hemme, Tong Yuan, Joy Van Nostrand, Liyou Wu, Xuedong Zhou, Wenyuan Shi, Lanjuan Li, Jian Xu, Jizhong Zhou*. “Development of HuMiChip for functional profiling of human microbiomes.” PloS ONE 9.3 (2014): e90546.

Qichao Tu, Zhili He, Ye Deng and Jizhong Zhou*. “Strain/Species-Specific Probe Design for Microbial Identification Microarrays.” Applied and Environmental Microbiology 79.16 (2013): 5085-5088.

Qichao Tu, Haitao Dong*, Haigen Yao, Yongqi Fang, Cheng'en Dai, Hongmei Luo, Jian Yao, Dong Zhao, and Debao Li*. "Global identification of significantly expressed genes in developing endosperm of rice by expression sequence tags and cDNA array approaches." Journal of Integrative Plant Biology 50, no. 9 (2008): 1078-1088.

Qichao Tu, Ye Deng, Jizhong Zhou, and Zhili He. “Development and evaluation of functional gene arrays with GeoChip as an example.” Microarrays: Current Technology, Innovations and Applications. Caister Academic Press, Norwich, UK.ISBN: 978-1-908230-49-2 (Book Chapter)

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Jiaxiong Zeng, Qichao Tu, Xiaoli Yu, Lu Qian, Cheng Wang, Longfei Shu, Fei Liu, Shengwei Liu, Zhijian Huang, Jianguo He, Qingyun Yan & Zhili He. PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes. Microbiome volume 10, Article number: 101 (2022)

Xianzhe Gong, Zhiyi Chen, Ye Deng, Duo Zhao, Ping Gao, Liang Zhang, Qichao Tu, Lingyun Qu, Liwen Zheng, Yong Zhang, Chao Song, Jihua Liu. Contrasting archaeal and bacterial community assembly processes and the importance of rare taxa along a depth gradient in shallow coastal sediments. Science of The Total Environment, Volume 852, 2022, 158411.

Changfei He, Jihua Liu, Rui Wang, Yuanning Li, Qiang Zheng, Fanglue Jiao, Chen He, Quan Shi, Yongle Xu, Rui Zhang, Helmuth Thomas, John Batt, Paul Hill, Marlon Lewis, Hugh Maclntyre, Longfei Lu, Qinghua Zhang, Qichao Tu, Tuo Shi, Feng Chen, Nianzhi Jiao. Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment, Water Research, Volume 216, 2022, 118281.

焦念志*, 刘纪化, 石拓, 张传伦, 张永雨, 郑强, 陈泉睿, 汤凯, 王誉泽, 董海良, 唐剑武, 叶思源, 董双林, 高坤山, 张继红, 薛强, 李琦, 贺志理, 屠奇超, 王法明, 黄小平, 白雁, 潘德炉. 2021. 实施海洋负排放 践行碳中和战略. 中国科学: 地球科学. 51(4): 632-643.

Chenchao Xu, Kaihang Zhang, Wanying Zhu, Jing Xiao, Chen Zhu, Naifang Zhang, Fangjian Yu, Shuyao Li, Chunwu Zhu, Qichao Tu, Xin Chen, Jianguo Zhu, Shuijin Hu, Roger T. Koide, Mary K. Firestone, Lei Cheng. 2020. Large losses of ammonium-nitrogen from a rice ecosystem under elevated CO2. Science Advances. Vol. 6, no. 42, eabb7433. 

Buzzard, Vanessa, Sean T. Michaletz, Ye Deng, Zhili He, Daliang Ning, Lina Shen, Qichao Tu, Joy D. Van Nostrand, James W. Voordeckers, Jianjun Wang, Michael D. Weiser, Michael Kaspari, Robert B. Waide, Jizhong Zhou, Brian J. Enquist*. 2019. “Continental Scale Structuring of Forest and Soil Diversity via Functional Traits.” Nature Ecology and Evolution 3 (9): 1298–1308.

Wu, Linwei, Daliang Ning, Bing Zhang, Yong Li, Ping Zhang, Xiaoyu Shan, Qiuting Zhang, Mathew Brown, Zhenxin Li, Joy D. Van Nostrand, Fangqiong Ling, Naijia Xiao, Ya Zhang, Julia Vierheilig, George F. Wells, Yunfeng Yang, Ye Deng, Qichau Tu, Aijie Wang, Tong Zhang, Zhili He, Jurg Keller, Per Halkjær Nielsen, Pedro J. J. Alvarez, Craig S. Criddle, Michael Wagner, James M. Tiedje, Qiang He, Thomas P. Curtis, David A Stahl, Lisa Alvarez-Cohen, Bruce E. Rittmann, Xianghua Wen, and Jizhong Zhou*. 2019. “Global Diversity and Biogeography of Bacterial Communities in Wastewater Treatment Plants.” Nature Microbiology 4 (7): 1183–95.

Shi, Zhou, Huaqun Yin, Joy D. Van Nostrand, James W. Voordeckers, Qichao Tu, Ye Deng, Mengting Yuan, Aifen Zhou, Ping Zhang, Naijia Xiao, Daliang Ning, Zhili He, Liyou Wu, and Jizhong Zhou. "Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities." Msystems 4, no. 4 (2019).

Ziyan Wei, Yueni Wu, Kai Feng, Min Yang, Yu Zhang, Qichao Tu, Jun Wang, Ye Deng. 2019. "ARGA, a pipeline for primer evaluation on antibiotic resistance genes." Environment international 128 (2019): 137-145.

Yan Li, Kun Wang, Bo Zhang, Qichao Tu, Yufei Yao, Bomiao Cui, Biao Ren, Jinzhi He, Xin Shen, Joy D. Van Nostrand, Jizhong Zhou, Wenyuan Shi, Liying Xiao, Changqing Lu, and Xuedong Zhou. 2019. "Salivary mycobiome dysbiosis and its potential impact on bacteriome shifts and host immunity in oral lichen planus." Int J Oral Sci 11, 13. 

Casey Chen, Chris Hemme, Joan Beleno, Zhou Jason Shi, Daliang Ning, Yujia Qin, Qichao Tu, Michael Jorgensen, Zhili He, Liyou Wu, and Jizhong Zhou. 2018. "Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy." The ISME journal, 12(5), pp.1210-1224.

He, Zhili, Ping Zhang, Linwei Wu, Andrea M. Rocha, Qichao Tu, Zhou Shi, Bo Wu, Yujia Qin, Jianjun Wang, Qingyun Yan, Daniel Curtis, Daliang Ning, Joy D. Van Nostrand, Liyou Wu, Yunfeng Yang, Dwayne A. Elias, David B. Watson, Michael W. W. Adams, Matthew W. Fields, Eric J. Alm, Terry C. Hazen, Paul D. Adams, Adam P. Arkin, and Jizhong Zhou*. 2018. “Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.” Mbio 9 (1).

Dai, Wenfang, Jinjie Zhang, Qichao Tu, Ye Deng, Qiongfen Qiu, and Jinbo Xiong. 2017. "Bacterioplankton assembly and interspecies interaction indicating increasing coastal eutrophication." Chemosphere 177: 317-325.

Ping Zhang, Zhili He, Joy D. Van Nostrand, Yujia Qin, Ye Deng, Liyou Wu, Qichao Tu, Jianjun Wang, Christopher W. Schad, Matthew W. Fields, Terry C. Hazen, Adam P. Arkin, David A. Stahl, and Jizhong Zhou. "Dynamic succession of groundwater sulfate-reducing communities during prolonged reduction of uranium in a contaminated aquifer." Environmental Science & Technology 51, no. 7 (2017): 3609-3620.

Cheng, Lei, Naifang Zhang, Mengting Yuan, Jing Xiao, Yujia Qin, Ye Deng, Qichao Tu, Kai Xue, Joy D. Van Nostrand, Liyou Wu, Zhili He, Xuhui Zhou, Mary Beth Leigh, Konstantinos T. Konstantinidis, Edward A.G. Schuur, Yiqi Luo, James M. Tiedje, Jizhong Zhou. 2017. “Warming Enhances Old Organic Carbon Decomposition through Altering Functional Microbial Communities.” The ISME Journal 11 (8): 1825–35.

Wang, Kun, Wenxin Lu, Qichao Tu, Yichen Ge, Jinzhi He, Yu Zhou, Yaping Gou, Joy D Van Nostrand,Yujia Qin, Jiyao Li, Jizhong Zhou, Yan Li, Liying Xiao & Xuedong Zhou. "Preliminary analysis of salivary microbiome and their potential roles in oral lichen planus." Scientific Reports 6 (2016): 22943.

Hemme, Christopher L., Qichao Tu, Zhou Shi, Yujia Qin, Weimin Gao, Ye Deng, Joy Van Nostrand et al. "Comparative metagenomics reveals impact of contaminants on groundwater microbiomes." Frontiers in Microbiology 6 (2015): 1205.

Deng, Ye, Ping Zhang, Yujia Qin, Qichao Tu, Yunfeng Yang, Zhili He, Christopher Warren Schadt, and Jizhong Zhou. "Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation." Environmental microbiology (2015).

Wu, Liyou, Chongqing Wen, Yujia Qin, Huaqun Yin, Qichao Tu, Joy D. Van Nostrand, Tong Yuan, Menting Yuan, Ye Deng, and Jizhong Zhou. "Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis." BMC Microbiology 15, no. 1 (2015): 125.

Aifen Zhou, Kristina Hillesland, Zhili He, Wendy Schackwitz, Qichao Tu, Grant Zane, Qiao Ma, Yuanyuan Qu, David Stahl, Judy Wall, Adam Arkin, Terry Hazen, and Matthew Fields, Jizhong Zhou. Rapid selective sweep of pre-existing polymorphismss and slow fixation of new mutations in Desulfovibrio vulgaris. ISME J (2015).

Chengwei Luo, Luis Rodriguez-R., Eric Johnston, Liyou Wu, Lei Cheng, Kai Xue, Qichao Tu, Ye Deng, Zhili He, Zhou Shi, mengting Yuan, Sherry Rebecca, dejun Li, Yiqi Luo, E.A.G. Schuur, Patrick Chain, James Tiedje, Jizhong Zhou, and Konstantinos Konstantinidis. “Soil microbial community responses to a decade of warming as revealed by comparative metagenomics”. Applied and Environmental Microbiology 80.5 (2014): 1777-1786.

Lu Lin, Yuetong Ji, Qichao Tu, Ranran Huang, Lin Teng, Xiaowei Zeng, Houhui Song, Kun Wang, Qian Zhou, Yifei Li, Qiu Cui, Zhili He, Jizhong Zhou, and Jian Xu. "Microevolution from shock to adaptation revealed strategies improving ethanol tolerance and production in thermophiles". Biotechnology for Biofuels 2013, 6:103

Fang YANG, Kang NING, Xingzhi CHANG, Xiao YUAN, Yue ZHANG, Xinping CUI, Qichao TU, Yuan TONG, Ye DENG, Christopher L Hemme, Joy Van Nostrand, Zhili HE, Jian Xu. "Saliva microbiota carry caries-specific functional gene signatures." PLoS ONE. 2014; 9(2):e76458.

Meiying Xu, Yun Fang, Jun Liu, Xingjuan Chen, Guoping Sun, Jun Guo, Zhengshuang Hua, Qichao Tu, Liyou Wu, Jizhong Zhou, and Xueduan Liu. Draft genome sequence of Shewanella decolorationis S12, a dye degrading bacterium isolated from a waste-water treatment plant. Genome Announcements 1.6 (2013): e00993-13.

Zhou, Aifen, He, Zhili, Qin, Yujia, Lu, Zhenmei, DENG, Ye, Tu, Qichao, Hemme, Christopher, Van Nostrand, Joy, Wu, Liyou, Hazen, Terry, Arkin, Adam, Zhou, Joe. “StressChip as a High Throughput Tool for Assessing Microbial Community Stability.” Environ Sci Technol. 2013 Sep 3;47(17):9841-9. 

Dongru Qiu, Hehong Wei, Qichao Tu, Yunfeng Yang, Ming Xie, Jingrong Chen, Mark Pinkerton, Yili Liang, Zhili He, and Jizhong Zhou. “Combined genomics and experimental analyses of respiratory characteristics of Shewanella putrefaciens W3-18-1.”  Appl Environ Microbiol. 2013 Sep;79(17):5250-7.

Lee, Y.-J., J. D. Van Nostrand, Q. Tu, T. Yuan, L. Cheng, Z. Lu, Y. Deng, M. Q. Carter, Z. He, L. Wu, F. Yang, J. Xu, and J. Zhou. 2013. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. The ISME J. 2013 Oct;7(10):1974-84.

Zhou, Jizhong, Liyou Wu, Ye Deng, Xiaoyang Zhi, Yi-Huei Jiang, Qichao Tu, Jianping Xie, Joy D. Van Nostrand, Zhili He, and Yunfeng Yang. "Reproducibility and quantitation of amplicon sequencing-based detection." The ISME journal 5, no. 8 (2011): 1303-1313.

Hemme, Christopher L., Matthew W. Fields, Qiang He, Ye Deng, Lu Lin, Qichao Tu, Housna Mouttaki et al. "Correlation of genomic and physiological traits of thermoanaerobacter species with biofuel yields." Applied and Environmental Microbiology 77, no. 22 (2011): 7998-8008.

Lin, Lu, Houhui Song, Qichao Tu, Yujia Qin, Aifen Zhou, Wenbin Liu, Zhili He, Jizhong Zhou, and Jian Xu. "The thermoanaerobacter glycobiome reveals mechanisms of pentose and hexose co-utilization in bacteria." PLoS Genetics 7, no. 10 (2011): e1002318.

Zhou, Jizhong, Ye Deng, Feng Luo, Zhili He, Qichao Tu, and Xiaoyang Zhi. "Functional molecular ecological networks." MBio 1, no. 4 (2010).

He, Zhili, Ye Deng, Joy D. Van Nostrand, Qichao Tu, Meiying Xu, Christopher L. Hemme, Xingyuan Li et al. "GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity." The ISME Journal 4, no. 9 (2010): 1167-1179.

Dong, HaiTao, XiaoQin Guo, YanXi Pei, ChengEn Dai, YongQi Fang, Qichao Tu, JieYun Zhuang, Dong Zhao, KangLe Zheng, and DeBao Li. "Multiple splicing types of OsRIX4, an RAD21 homolog in rice (Oryza sativa L.)." Chinese Science Bulletin 52, no. 11 (2007): 1468-1474.

Jiaofang Shao, Qichao Tu, Ming Chen. Comprehensive Computational Analysis Approach for Alzheimer's Disease. Bioinformatics and Biomedical Engineering, 2007. ICBBE 2007. The 1st International Conference on; 08/2007